This pilot study examined knowledge, understanding and perceived acceptability of key methodological concepts in clinical trials among injecting drug users (IDUs) in Sydney, Australia. Participants were clinical trial-experienced (n = 17) and trial-naïve (n = 99) IDUs recruited from community needle and syringe programs, and through institutions involved in clinical trials with IDU participants. Cross-sectional data were collected via a study-specific interviewer-administered survey. Following detailed verbal explanations, higher proportions of trial-experienced than trial-naïve participants demonstrated an understanding of all clinical trial concepts assessed, including single blinding (94% versus 60%); placebo (94% versus 49%); equipoise (71% versus 60%); comparison (59% versus 46%); randomisation (59% versus 21%); and double blinding (47% versus 3%). Multivariate analyses indicated a better understanding among trial-experienced participants. Participants who demonstrated an understanding of 'placebo' and 'double blinding' were significantly more likely to perceive these concepts to be acceptable than those who did not. Results indicate the need for targeted education programs that adequately inform IDUs about clinical trial concepts prior to recruitment to a clinical trial, and support adaptations of informed consent procedures to ensure trial participants' comprehensive understanding of methodologies and their implications.